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Abstract
Obesity is a multi-factorial disease that is influenced by genetic, epigenetic, and environmental factors. Precision medicine is a practice wherein prevention and treatment strategies take individual variability into account. It involves using a variety of factors including deep phenotyping using clinical, physiologic, and behavioral characteristics, 'omics assays (eg, genomics, epigenomics, transcriptomics, and microbiomics among others), and environmental factors to devise practices that are individualized to subsets of patients. Personalizing the therapeutic modality to the individual can lead to enhanced effectiveness and tolerability. The authors review advances in precision medicine made in the field of bariatrics and discuss future avenues and challenges.
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Affiliation(s)
- Khushboo Gala
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55902, USA. https://twitter.com/KhushbooSGala
| | - Wissam Ghusn
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55902, USA; Department of Internal Medicine, Boston University Medical Center, Harrison Avenue, Boston, MA 02111, USA. https://twitter.com/Wissam_Ghusn
| | - Andres Acosta
- Precision Medicine for Obesity Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55902, USA.
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Xu F, Li Z, Liu T, Pang X, Fan C, Jiang H. The role of cellular senescence in the pathogenesis of Rheumatoid Arthritis: Focus on IL-6 as a target gene. Cytokine 2024; 184:156762. [PMID: 39326197 DOI: 10.1016/j.cyto.2024.156762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 08/30/2024] [Accepted: 09/13/2024] [Indexed: 09/28/2024]
Abstract
BACKGROUND Rheumatoid arthritis is a chronic autoimmune disease. However, the specific role of senescence in rheumatoid arthritis (RA) is unknown. This study aimed to identify potential aging-related genes that have diagnostic and therapeutic value for RA. METHODS The GSE89408 dataset was downloaded from the Gene Expression Omnibus (GEO). Aging-related genes were downloaded from the HAGR database. Differentially expressed genes (DEGs) were subsequently identified with the "edgeR" tool. Next, hub genes were identified with a PPI network and CytoHubba analysis. Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic value of these hub genes. Immune infiltration analysis was performed with the CIBERSORT algorithm. Additionally, molecular docking was performed with CB-Dock2. Finally, correlation experiments were performed to validate the bioinformatics and molecular docking results. RESULTS A total of 22 ADEGs were identified. Combined PPI network and CytoHubba analyses identified a total of 7 hub genes, including IL-6, IL7R, IL2RG, CDK1, PTGS2, and LEP, which are associated mainly with inflammation and immune responses. ROC analysis revealed that the hub genes were highly predictive of RA. Analysis of immune infiltration revealed that the 6 hub genes were positively associated with M1 macrophages. Validation experiments revealed that the inhibition of IL-6 significantly decreased the degree of synovial fibroblast (FLS) senescence. Furthermore, molecular docking and validation experiments revealed that IL-6 is a potential target for drug therapy. CONCLUSION This study demonstrated that RA-FLS senescence may promote the development of RA via inflammatory and immune mechanisms. Seven hub genes were identified, of which IL-6 is a reliable biomarker for the diagnosis and treatment of RA.
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Affiliation(s)
- Fengxia Xu
- Clinical Research Experiment Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230012, Anhui, China; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, Anhui, China
| | - Zhen Li
- Clinical Research Experiment Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230012, Anhui, China; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, Anhui, China
| | - Tao Liu
- Clinical Research Experiment Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230012, Anhui, China; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, Anhui, China
| | - Xue Pang
- Clinical Research Experiment Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230012, Anhui, China; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, Anhui, China
| | - Chang Fan
- Clinical Research Experiment Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230012, Anhui, China
| | - Hui Jiang
- Clinical Research Experiment Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230012, Anhui, China; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, Anhui, China.
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Mahjoubin-Tehran M, Atkin SL, Jamialahmadi T, Kroh M, Eid AH, Almahmeed W, Sahebkar A. The differential expression of adipose tissue genes in short, medium and long-term periods after bariatric surgery. Sci Rep 2024; 14:19991. [PMID: 39198660 PMCID: PMC11358539 DOI: 10.1038/s41598-024-70629-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
Bariatric surgery is an approved treatment for obesity that consistently improves metabolic syndrome, with well-documented beneficial effects on dyslipidemia, cardiovascular risk, nonalcoholic fatty liver disease and glucose homeostasis. In this study, we determined the differential expression genes in three periods after bariatric surgery: short-term (4-months), medium-term (1- and 2-years), and long-term (5-years) periods. Two microarray profiles were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified by comparing the expression of adipose tissue genes before surgery compared to short, medium and long-term periods following surgery. Shared DEGs for the medium-term were evaluated by comparing the DEGs for both 1 and 2 years. 165, 65, and 59 DEGs were identified in short-medium-long periods. The protein-protein interactions were analyzed by STRING. A co-expression network was constructed by mapping the DEGs onto the GeneMANIA plugin of Cytoscape. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) and wikipathway analysis were done for each group of DEGs. Interleukin-8 receptor activity, complement receptor activity and opsonin receptor activity/N-formyl peptide receptor activity in GO Function enrichment and cellular response to interleukin-8, positive regulation of hippocampal neuron apoptotic process, and positive regulation of hippocampal neuron apoptotic process in GO Process showed the best scores in short-, medium-, and long-term periods, respectively. Eight genes, including CCL2 (Chemokine ligand 2), CXCR4 (CXC motif chemokine receptor 4), EGR2 (Early Growth Response 2), FPR1 (Formyl Peptide Receptor 1), IL6 (interleukin-6), RGS2 (regulator of gene protein signaling2), SELPLG (Selectin P Ligand), and THBS1 (Thrombospondin 1) were identified as shared DEGs in the three periods after surgery. Importantly, results of DAVID database analysis showed 7, 6, 4, and 4 of these genes have roles in immune/ cancer/cardiovascular diseases, type 2 diabetes, myocardial infarct, and atherosclerosis, respectively.
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Affiliation(s)
| | - Stephen L Atkin
- Royal College of Surgeons in Ireland, Bahrain, PO Box 15503, Adliya, Bahrain
| | - Tannaz Jamialahmadi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Matthew Kroh
- Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ali H Eid
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Wael Almahmeed
- Heart and Vascular Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Yuan L, Zhang L, Liu X, Li S, Zou J. Identification of differential immune cells and related diagnostic genes in patients with diabetic retinopathy. Medicine (Baltimore) 2023; 102:e35331. [PMID: 37773794 PMCID: PMC10545100 DOI: 10.1097/md.0000000000035331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Diabetic retinopathy (DR) is a frequent microvascular abnormality associated with diabetes mellitus. The loss of retinal immunity is an important underlying mechanism of the DR pathogenesis, including the change in retinal immunosuppressive characteristics and the blood-retinal barrier disturbances. Therefore, this investigation screens immune-associated biomarkers in the retina of DR patients. METHODS In this investigation, the differential expression genes (DEGs) were acquired from Gene Expression Omnibus data GSE102485. The relative expression of 22 immune cell types in each sample was calculated by CIBERSORT analysis based on gene expression profile. The core module closely associated with immune infiltration was also screened by weighted gene co-expression network analysis (WGCNA). The overlapping DEGs and module genes were the differentially expressed immune-related genes (DEIRGs). With the help of the genes/proteins (STRING) database and MCODE plug-in, the protein-protein interaction (PPI) network hub genes were screened. Furthermore, the miRNA-hub genes and transcription factor (TF)-hub gene regulatory network were used to explain the possible signal pathways in DR. The hub genes verification was carried out by Polymerase Chain Reaction. Lastly, select CSF1R and its related pathway factor p-ERK1/2 to verify their expression in RF/6A under normal and high glucose environments. RESULTS A total of 3583 principle DEGs, that enriched immune-related GO terms and infection-related pathways were identified. CIBERSORT analysis showed that naive B cells, M2 macrophages, eosinophils, and neutrophil infiltration were significantly different. After intersecting 3583 DEGs, 168 DEIRGs and 181 module genes were identified. Furthermore, 15 hub genes, TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86, were identified via PPI network. The identified hub genes were up-regulated in DR and showed a high DR diagnostic value. Regulatory networks of the miRNA- and TF-hub genes can help understand the etiology of disease at the genetic level and optimize treatment strategy. CD14, VSIG4, HCK, and CSF1R were verified to be highly expressed in the vitreous of patients with DR. n RF/6A, CSF1R, and p-ERK1/2 were significantly overexpressed under high glucose conditions, with a statistically significant difference. CONCLUSION This investigation identified 15 genes (TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86) as hub DR genes, which may serve as a new potential point for the diagnosis and treatment of DR. CSF1R/p-ERK1/2 signaling may promotes the development of retinal neovascularization.
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Affiliation(s)
- LinHui Yuan
- Department of Ophthalmology, the Third People’s Hospital Affiliated to Dalian Medical University, Dalian, Liaoning, China
- Dalian Medical University, Dalian, Liaoning, China
| | - LiJun Zhang
- Department of Ophthalmology, the Third People’s Hospital Affiliated to Dalian Medical University, Dalian, Liaoning, China
- Dalian Medical University, Dalian, Liaoning, China
| | - Xin Liu
- Department of Ophthalmology, the Third People’s Hospital Affiliated to Dalian Medical University, Dalian, Liaoning, China
- Dalian Medical University, Dalian, Liaoning, China
| | - Sheng Li
- Department of Ophthalmology, the Third People’s Hospital Affiliated to Dalian Medical University, Dalian, Liaoning, China
- Dalian Medical University, Dalian, Liaoning, China
| | - JiXin Zou
- Department of Ophthalmology, the Third People’s Hospital Affiliated to Dalian Medical University, Dalian, Liaoning, China
- Dalian Medical University, Dalian, Liaoning, China
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Herstowska M, Przygocka-Pieniążek A, Grabowski K, Kaska Ł. Prevalence of mental disorders in patients with pathological obesity selected for bariatric surgery in the KOS-BAR nationwide multi-centre pilot programme - a preliminary report. Wideochir Inne Tech Maloinwazyjne 2023; 18:502-509. [PMID: 37868291 PMCID: PMC10585463 DOI: 10.5114/wiitm.2023.128910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/14/2023] [Indexed: 10/24/2023] Open
Abstract
Obesity affects over 600,000 people in Poland, and bariatric surgery is a vital part of the multidisciplinary approach to treatment. To improve outcomes, Poland's public health institutions implemented the KOS-BAR programme, a multicentre nationwide pilot initiative that includes psychiatric evaluations of patients. The aim of this study was to assess the prevalence of mental disorders, verify diagnoses, and evaluate pharmacotherapy efficacy for patients under psychiatric treatment and selected for bariatric surgery. Of the 180 patients evaluated, 40% had a history of mental disorders, with depressive and eating disorders being the most common diagnoses. Patients selected for revision surgery had a higher incidence of depressive and compulsive eating disorders. Psychiatric support can improve patient cooperation and optimize long-term outcomes after bariatric surgery. A more complete evaluation of the psychological profile and depressive disorder's impact on bariatric treatment outcomes will be the next step for this group of patients.
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Affiliation(s)
- Marta Herstowska
- Department of Pediatrics, Diabetology and Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Ada Przygocka-Pieniążek
- Department of Pediatrics, Diabetology and Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Karol Grabowski
- Department of Psychiatry, Medical University of Gdansk, Gdansk, Poland
| | - Łukasz Kaska
- Department of Oncological, Transplant and General Surgery, Medical University of Gdansk, Gdansk, Poland
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Zheng K, Yang W, Wang S, Sun M, Jin Z, Zhang W, Ren H, Li C. Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques. Sci Rep 2023; 13:14153. [PMID: 37644056 PMCID: PMC10465496 DOI: 10.1038/s41598-023-40530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
Atherosclerosis is a chronic lipid-driven inflammatory response of the innate and adaptive immune systems, and it is responsible for several cardiovascular ischemic events. The present study aimed to determine immune infiltration-related biomarkers in carotid atherosclerotic plaques (CAPs). Gene expression profiles of CAPs were extracted from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between the CAPs and control groups were screened by the "limma" package in R software. Immune cell infiltration between the CAPs and control groups was evaluated by the single sample gene set enrichment analysis. Key infiltrating immune cells in the CAPs group were screened by the Wilcoxon test and least absolute shrinkage and selection operator regression. The weighted gene co-expression network analysis was used to identify immune cell-related genes. Hub genes were identified by the protein-protein interaction (PPI) network. Receiver operating characteristic curve analysis was performed to assess the gene's ability to differentiate between the CAPs and control groups. Finally, we constructed a miRNA-gene-transcription factor network of hub genes by using the ENCODE database. Eleven different types of immune infiltration-related cells were identified between the CAPs and control groups. A total of 1,586 differentially expressed immunity-related genes were obtained through intersection between DEGs and immune-related genes. Twenty hub genes were screened through the PPI network. Eventually, 7 genes (BTK, LYN, PTPN11, CD163, CD4, ITGAL, and ITGB7) were identified as the hub genes of CAPs, and these genes may serve as the estimable drug targets for patients with CAPs.
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Affiliation(s)
- Kai Zheng
- Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Wentao Yang
- Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Shengxing Wang
- Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Mingsheng Sun
- Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Zhenyi Jin
- Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Wangde Zhang
- Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Hualiang Ren
- Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.
| | - Chunmin Li
- Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.
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Ge S, Hu J, Gao S, Ren J, Zhu G. LncRNA NEAT1: A novel regulator associated with the inflammatory response in acute respiratory distress syndrome. Gene 2023:147582. [PMID: 37353041 DOI: 10.1016/j.gene.2023.147582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/31/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a life-threatening condition with an unfavorable prognosis. As the pathogenesis of ARDS remains unclear, we aimed to identify the core genes associated with ARDS and the mechanisms by which competing endogenous RNAs (ceRNAs) regulate the disease's progression. METHODS Three mRNA microarray datasets (GSE17355, GSE48787, and GSE130936), derived from the Gene Expression Omnibus (GEO) database, were selected. Common differentially expressed genes (DEGs) related to acute lung injury (ALI) were identified and subjected to enrichment analysis. Then, hub genes were figured out through the protein-protein interaction (PPI) network and functional analysis, and targeted miRNAs and lncRNAs were predicted. Finally, the ceRNA networks associated with ALI were constructed and validated experimentally. RESULTS A total of 155 upregulated and 93 downregulated DEGs were identified in the three datasets. The TNF signaling pathway and IL-17 signaling pathway were the most enriched pathways. Then, eleven DEGs enriched in the IL-17 signaling pathway were selected as the hub genes. Three miRNAs (mmu-mir-155-5p, mmu-mir-21a-5p, and mmu-mir-122-5p), which were located in the lung tissue and predicted to bind the hub genes at the same time, and two lncRNAs (Neat1 and Tug1), which have binding sites for the aforementioned miRNAs, were filtered. With qPCR verification, we identified a ceRNA network composed of NEAT1, miR-21-5p, MMP9, and CXCL5. NEAT1 knockdown promoted the migration and reduced the expression of pro-inflammatory factor and reactive oxygen species (ROS) in lung epithelial cells. We eventually confirmed that NEAT1/miR-21-5p/CXCL5/MMP9 played a pivotal role in regulating the inflammatory response in ALI. CONCLUSION The IL-17 signaling pathway is of great importance in the pathogenesis of ARDS. NEAT1/miR-21-5p is involved in the inflammation of ALI by regulating CXCL5 and MMP9.
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Affiliation(s)
- Shanhui Ge
- Department of Respiratory and Critical Care Medicine, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Jiaxin Hu
- Department of Respiratory and Critical Care Medicine, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Shijuan Gao
- Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University
| | - Jianwei Ren
- Department of Respiratory and Critical Care Medicine, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Guangfa Zhu
- Department of Respiratory and Critical Care Medicine, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
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Duarte GCK, Pellenz F, Crispim D, Assmann TS. Integrated bioinformatics approach reveals methylation-regulated differentially expressed genes in obesity. ARCHIVES OF ENDOCRINOLOGY AND METABOLISM 2023; 67:e000604. [PMID: 37252693 PMCID: PMC10665070 DOI: 10.20945/2359-3997000000604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/08/2022] [Indexed: 05/31/2023]
Abstract
Objective To identify DNA methylation and gene expression profiles involved in obesity by implementing an integrated bioinformatics approach. Materials and methods Gene expression (GSE94752, GSE55200, and GSE48964) and DNA methylation (GSE67024 and GSE111632) datasets were obtained from the GEO database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in subcutaneous adipose tissue of patients with obesity were identified using GEO2R. Methylation-regulated DEGs (MeDEGs) were identified by overlapping DEGs and DMGs. The protein-protein interaction (PPI) network was constructed with the STRING database and analyzed using Cytoscape. Functional modules and hub-bottleneck genes were identified by using MCODE and CytoHubba plugins. Functional enrichment analyses were performed based on Gene Ontology terms and KEGG pathways. To prioritize and identify candidate genes for obesity, MeDEGs were compared with obesity-related genes available at the DisGeNET database. Results A total of 54 MeDEGs were identified after overlapping the lists of significant 274 DEGs and 11,556 DMGs. Of these, 25 were hypermethylated-low expression genes and 29 were hypomethylated-high expression genes. The PPI network showed three hub-bottleneck genes (PTGS2, TNFAIP3, and FBXL20) and one functional module. The 54 MeDEGs were mainly involved in the regulation of fibroblast growth factor production, the molecular function of arachidonic acid, and ubiquitin-protein transferase activity. Data collected from DisGeNET showed that 11 of the 54 MeDEGs were involved in obesity. Conclusion This study identifies new MeDEGs involved in obesity and assessed their related pathways and functions. These results data may provide a deeper understanding of methylation-mediated regulatory mechanisms of obesity.
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Affiliation(s)
- Guilherme Coutinho Kullmann Duarte
- Serviço de Endocrinologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
- Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Felipe Pellenz
- Serviço de Endocrinologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
- Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Daisy Crispim
- Serviço de Endocrinologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
- Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil,
| | - Tais Silveira Assmann
- Serviço de Endocrinologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
- Programa de Pós-graduação em Ciências Médicas: Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
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Chen X, Xie L, Jiang Y, Zhang R, Wu W. LCK, FOXC1 and hsa-miR-146a-5p as potential immune effector molecules associated with rheumatoid arthritis. Biomarkers 2023; 28:130-138. [PMID: 36420648 DOI: 10.1080/1354750x.2022.2150315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rheumatoid arthritis (RA) is a type of systemic immune disease characterized by chronic inflammatory disease of the joints. However, the aetiology and underlying molecular events of RA are unclear. Here, we applied bioinformatics analysis to identify potential immune effector molecules involved in RA. The three microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database. We used the R software screen 115 overlapping differentially expressed genes (DEGs). Subsequently, we constructed a protein-protein interaction (PPI) network encoded by these DEGs and identified 10 genes closely associated with RA - LCK, GZMA, GZMB, CD2, LAG3, IL-15, TNFRSF4, CD247, CCR5 and CCR7. Furthermore, in the miRNA-hub gene networks, we screened out hsa-miR-146a-5p, which is the miRNA controlling the largest number of hub genes. Finally, we found some transcription factors that closely interact with hub genes, such as FOXC1, GATA2, YY1, RUNX2, SREBF1, CEBPB and NFIC. This study successfully predicted that LCK, FOXC1 and hsa-miR-146a-5p can be used as potential immune effector molecules of RA. Our study may have potential implications for future prediction of disease progression in patients with symptomatic RA, and has important significance for the pathogenesis and targeted therapy of RA.
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Affiliation(s)
- Xuemeng Chen
- Department of Traditional Chinese Medicine and rheumatism immunology, the First Affiliated Hospital of Army Medical University, Chongqing City, China
| | - Li Xie
- Department of Traditional Chinese Medicine, Chongqing Dadukou District People's Hospital, Chongqing City, China
| | - Yi Jiang
- Department of Traditional Chinese Medicine and rheumatism immunology, the First Affiliated Hospital of Army Medical University, Chongqing City, China
| | - Ronghua Zhang
- Department of Traditional Chinese Medicine and rheumatism immunology, the First Affiliated Hospital of Army Medical University, Chongqing City, China
| | - Wei Wu
- Department of Traditional Chinese Medicine and rheumatism immunology, the First Affiliated Hospital of Army Medical University, Chongqing City, China
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Ziqubu K, Dludla PV, Moetlediwa MT, Nyawo TA, Pheiffer C, Jack BU, Nkambule B, Mazibuko-Mbeje SE. Disease progression promotes changes in adipose tissue signatures in type 2 diabetic (db/db) mice: The potential pathophysiological role of batokines. Life Sci 2023; 313:121273. [PMID: 36521548 DOI: 10.1016/j.lfs.2022.121273] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/03/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022]
Abstract
Unlike the white adipose tissue (WAT) which mainly stores excess energy as fat, brown adipose tissue (BAT) has become physiologically important and therapeutically relevant for its prominent role in regulating energy metabolism. The current study makes use of an established animal model of type 2 diabetes (T2D) db/db mice to determine the effect of the disease progression on adipose tissue morphology and gene regulatory signatures. Results showed that WAT and BAT from db/db mice display a hypertrophied phenotype that is consistent with increased expression of the pro-inflammatory cytokine, tumor necrosis factor-alpha (Tnf-α). Moreover, BAT from both db/db and non-diabetic db/+ control mice displayed an age-related impairment in glucose homeostasis, inflammatory profile, and thermogenic regulation, as demonstrated by reduced expression of genes like glucose transporter (Glut-4), adiponectin (AdipoQ), and uncoupling protein 1 (Ucp-1). Importantly, gene expression of the batokines regulating sympathetic neurite outgrowth and vascularization, including bone morphogenic protein 8b (Bmp8b), fibroblast growth factor 21 (Fgf-21), neuregulin 4 (Nrg-4) were altered in BAT from db/db mice. Likewise, gene expression of meteorin-like (Metrnl), growth differentiation factor 15 (Gdt-15), and C-X-C motif chemokine-14 (Cxcl-14) regulating pro- and anti-inflammation were altered. This data provides some new insights into the pathophysiological mechanisms involved in BAT hypertrophy (or whitening) and the disturbances of batokines during the development and progression of T2D. However, these are only preliminary results as additional experiments are necessary to confirm these findings in other experimental models of T2D.
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Affiliation(s)
- Khanyisani Ziqubu
- Department of Biochemistry, North-West University, Mmabatho 2745, South Africa
| | - Phiwayinkosi V Dludla
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa; Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Marakiya T Moetlediwa
- Department of Biochemistry, North-West University, Mmabatho 2745, South Africa; Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | - Thembeka A Nyawo
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa; Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, University of Stellenbosch, Tygerberg 7505, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa; Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, University of Stellenbosch, Tygerberg 7505, South Africa; Department of Obstetrics and Gynaecology, Faculty of Health Science, University of Pretoria, Pretoria 0001, South Africa
| | - Babalwa U Jack
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | - Bongani Nkambule
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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Ma X, Zhang X, Leng T, Ma J, Yuan Z, Gu Y, Hu T, Liu Q, Shen T. Identification of Oxidative Stress-Related Biomarkers in Diabetic Kidney Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:1067504. [PMID: 36624863 PMCID: PMC9825216 DOI: 10.1155/2022/1067504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 01/02/2023]
Abstract
BACKGROUND Diabetic kidney disease (DKD) is a leading cause of end-stage renal disease throughout the world. In kidney disease, oxidative stress has been linked to both antioxidant depletions and increased reactive oxygen species (ROS) production. Thus, the objective of this study was to identify biomarkers related to oxidative stress in DKD. METHODS The gene expression profile of the DKD was extracted from the Gene Expression Omnibus (GEO) database. The identification of the differentially expressed genes (DEGs) was performed using the "limma" R package, and weighted gene coexpression network analysis (WGCNA) was used to find the gene modules that were most related to DKD. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed using "Org.Hs.eg.db" R package. The protein-protein interaction (PPI) network was constructed using the STRING database. The hub genes were identified by the Molecular Complex Detection (MCODE) plug-in of Cytoscape software. The diagnostic capacity of hub genes was verified using the receiver operating characteristic (ROC) curve. Correlations between diagnostic genes were analyzed using the "corrplot" package. In addition, the miRNA gene transcription factor (TF) network was used to explain the regulatory mechanism of hub genes in DKD. RESULTS DEGs analysis and WGCNA-identified 160 key genes were identified in DKD patients. Among them, nine oxidative stress-related genes were identified as candidate hub genes for DKD. Using the PPI network, five hub genes, NR4A2, DUSP1, FOS, JUN, and PTGS2, were subsequently identified. All the hub genes were downregulated in DKD and had a high diagnostic value of DKD. The regulatory mechanism of hub genes was analyzed from the miRNA gene-TF network. CONCLUSION Our study identified NR4A2, DUSP1, FOS, JUN, and PTGS2 as hub genes of DKD. These genes may serve as potential therapeutic targets for DKD patients.
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Affiliation(s)
- Xiaoju Ma
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaobo Zhang
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tian Leng
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jingru Ma
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhongzhu Yuan
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yalin Gu
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tingting Hu
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qiuyan Liu
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tao Shen
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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12
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Zhao Z, Wang C, Jia J, Wang Z, Li L, Deng X, Cai Z, Yang L, Wang D, Ma S, Zhao L, Tu Z, Yuan G. Regulatory network of metformin on adipogenesis determined by combining high-throughput sequencing and GEO database. Adipocyte 2022; 11:56-68. [PMID: 34974794 PMCID: PMC8741290 DOI: 10.1080/21623945.2021.2013417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Adipose differentiation and excessive lipid accumulation are the important characteristics of obesity. Metformin, as a classic hypoglycaemic drug, has been proved to reduce body weight in type 2 diabetes, the specific mechanism has not been completely clear. A few studies have explored its effect on adipogenesis in vitro, but the existing experimental results are ambiguous. 3T3-L1 preadipocytes were used to explore the effects of metformin on the morphological and physiological changes of lipid droplets during adipogenesis. A high throughput sequencing was used to examine the effects of metformin on the transcriptome of adipogenesis. Considering the inevitable errors among independent experiments, we performed integrated bioinformatics analysis to identify important genes involved in adipogenesis and reveal potential molecular mechanisms. During the process of adipogenesis, metformin visibly relieved the morphological and functional changes. In addition, metformin reverses the expression pattern of genes related to adipogenesis at the transcriptome level. Combining with integrated bioinformatics analyses to further identify the potential targeted genes regulated by metformin during adipogenesis. The present study identified novel changes in the transcriptome of metformin in the process of adipogenesis that might shed light on the underlying mechanism by which metformin impedes the progression of obesity.
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Affiliation(s)
- Zhicong Zhao
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Chenxi Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jue Jia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhaoxiang Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Lian Li
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xia Deng
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhensheng Cai
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ling Yang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dong Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Suxian Ma
- Department of Endocrinology, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Li Zhao
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhigang Tu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Guoyue Yuan
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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Cruz-García EM, Frigolet ME, Canizales-Quinteros S, Gutiérrez-Aguilar R. Differential Gene Expression of Subcutaneous Adipose Tissue among Lean, Obese, and after RYGB (Different Timepoints): Systematic Review and Analysis. Nutrients 2022; 14:nu14224925. [PMID: 36432612 PMCID: PMC9693162 DOI: 10.3390/nu14224925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/23/2022] Open
Abstract
The main roles of adipose tissue include triglycerides storage and adipokine secretion, which regulate energy balance and inflammation status. In obesity, adipocyte dysfunction leads to proinflammatory cytokine production and insulin resistance. Bariatric surgery is the most effective treatment for obesity, the gold-standard technique being Roux-en-Y gastric bypass (RYGB). Since metabolic improvements after RYGB are clear, a better understanding of adipose tissue molecular modifications could be derived from this study. Thus, the aim of this systematic review was to find differentially expressed genes in subcutaneous adipose tissue of lean, obese and post-RYGB (distinct timepoints). To address this objective, publications from 2015-2022 reporting gene expression (candidate genes or transcriptomic approach) of subcutaneous adipose tissue from lean and obese individuals before and after RGYB were searched in PubMed, Elsevier, and Springer Link. Excluded publications were reviews, studies analyzing serum, other types of tissues, or bariatric procedures. A risk-of-bias summary was created for each paper using Robvis, to finally include 17 studies. Differentially expressed genes in post-RYGB vs. obese and lean vs. obese were obtained and the intersection among these groups was used for analysis and gene classification by metabolic pathway. Results showed that the lean state as well as the post-RYGB is similar in terms of increased expression of insulin-sensitizing molecules, inducing lipogenesis over lipolysis and downregulating leukocyte activation, cytokine production and other factors that promote inflammation. Thus, massive weight loss and metabolic improvements after RYGB are accompanied by gene expression modifications reverting the "adipocyte dysfunction" phenomenon observed in obesity conditions.
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Affiliation(s)
- Elena Marisol Cruz-García
- Laboratorio de Investigación en Enfermedades Metabólicas: Obesidad y Diabetes, Hospital Infantil de México “Federico Gómez”, Mexico City 06720, Mexico
| | - María E. Frigolet
- Laboratorio de Investigación en Enfermedades Metabólicas: Obesidad y Diabetes, Hospital Infantil de México “Federico Gómez”, Mexico City 06720, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genόmica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genόmica (INMEGEN), Mexico City 14610, Mexico
| | - Ruth Gutiérrez-Aguilar
- Laboratorio de Investigación en Enfermedades Metabólicas: Obesidad y Diabetes, Hospital Infantil de México “Federico Gómez”, Mexico City 06720, Mexico
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
- Correspondence: ; Tel.: +52-5552289917 (ext. 4509)
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14
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Tai Y, Tian H, Yang X, Feng S, Chen S, Zhong C, Gao T, Gang X, Liu M. Identification of hub genes and candidate herbal treatment in obesity through integrated bioinformatic analysis and reverse network pharmacology. Sci Rep 2022; 12:17113. [PMID: 36224334 PMCID: PMC9556576 DOI: 10.1038/s41598-022-22112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/10/2022] [Indexed: 01/04/2023] Open
Abstract
Obesity is a global epidemic elevating the risk of various metabolic disorders. As there is a lack of effective drugs to treat obesity, we combined bioinformatics and reverse network pharmacology in this study to identify effective herbs to treat obesity. We identified 1011 differentially expressed genes (DEGs) of adipose tissue after weight loss by analyzing five expression profiles (GSE103766, GSE35411, GSE112307, GSE43471, and GSE35710) from the Gene Expression Omnibus (GEO) database. We identified 27 hub genes from the protein-protein interaction (PPI) network by performing MCODE using the Search Tool for the Retrieval of Interacting Genes (STRING) database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that these hub genes have roles in the extracellular matrix-receptor interaction, cholesterol metabolism, PI3K-Akt signaling pathway, etc. Ten herbs (Aloe, Portulacae Herba, Mori Follum, Silybum Marianum, Phyllanthi Fructus, Pollen Typhae, Ginkgo Semen, Leonuri Herba, Eriobotryae Folium, and Litseae Fructus) targeting the nine hub genes (COL1A1, MMP2, MMP9, SPP1, DNMT3B, MMP7, CETP, COL1A2, and MUC1) using six ingredients were identified as the key herbs. Quercetin and (-)-epigallocatechin-3-gallate were determined to be the key ingredients. Lastly, Ingredients-Targets, Herbs-Ingredients-Targets, and Herbs-Taste-Meridian Tropism networks were constructed using Cytoscape to elucidate this complex relationship. This study could help identify promising therapeutic targets and drugs to treat obesity.
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Affiliation(s)
- Yuxing Tai
- grid.440665.50000 0004 1757 641XChangchun University of Chinese Medicine, Changchun, 130117 China
| | - Hongying Tian
- grid.440665.50000 0004 1757 641XChangchun University of Chinese Medicine, Changchun, 130117 China
| | - Xiaoqian Yang
- grid.440665.50000 0004 1757 641XJilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 China
| | - Shixing Feng
- grid.24695.3c0000 0001 1431 9176Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Shaotao Chen
- grid.440665.50000 0004 1757 641XDepartment of Acupuncture and Tuina, Changchun University of Chinese Medicine, Changchun, 130117 China ,grid.440665.50000 0004 1757 641XAcupuncture and Massage Center of the Third Affiliated Clinical Hospital, Changchun University of Chinese Medicine, Changchun, 130117 China
| | - Chongwen Zhong
- grid.440665.50000 0004 1757 641XDepartment of Acupuncture and Tuina, Changchun University of Chinese Medicine, Changchun, 130117 China
| | - Tianjiao Gao
- grid.440665.50000 0004 1757 641XChangchun University of Chinese Medicine, Changchun, 130117 China
| | - Xiaochao Gang
- grid.440665.50000 0004 1757 641XDepartment of Acupuncture and Tuina, Changchun University of Chinese Medicine, Changchun, 130117 China
| | - Mingjun Liu
- grid.440665.50000 0004 1757 641XDepartment of Acupuncture and Tuina, Changchun University of Chinese Medicine, Changchun, 130117 China ,grid.440665.50000 0004 1757 641XAcupuncture and Massage Center of the Third Affiliated Clinical Hospital, Changchun University of Chinese Medicine, Changchun, 130117 China
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15
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Soldo AM, Soldo I, Karačić A, Konjevod M, Perkovic MN, Glavan TM, Luksic M, Žarković N, Jaganjac M. Lipid Peroxidation in Obesity: Can Bariatric Surgery Help? Antioxidants (Basel) 2022; 11:antiox11081537. [PMID: 36009256 PMCID: PMC9405425 DOI: 10.3390/antiox11081537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Obesity and chronic oxidative stress, often being associated with each other in a vicious circle, are important factors of chronic diseases. Although it was usually considered to accompany aging and wealth, global trends show the increase in obesity among children even in Third World countries. Being manifested by an imbalance between energy consumption and food intake, obesity is characterized by an excessive or abnormal fat accumulation, impaired redox homeostasis and metabolic changes often associated with the self-catalyzed lipid peroxidation generating 4-hydroxynonenal, pluripotent bioactive peroxidation product of polyunsaturated fatty acids. Conservative methods targeting obesity produced only modest and transient results in the treatment of morbid obesity. Therefore, in recent years, surgery, primarily bariatric, became an attractive treatment for morbid obesity. Since adipose tissue is well known as a stress organ with pronounced endocrine functions, surgery results in redox balance and metabolic improvement of the entire organism. The source of bioactive lipids and lipid-soluble antioxidants, and the complex pathophysiology of lipid peroxidation should thus be considered from the aspects of personalized and integrative biomedicine to treat obesity in an appropriate way.
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Affiliation(s)
- Ana Maria Soldo
- Department of Gastroenterology, General Hospital “Dr. Ivo Pedisic”, 44000 Sisak, Croatia
| | - Ivo Soldo
- Surgery Clinic, University Hospital Sveti Duh, 10000 Zagreb, Croatia
| | - Andrija Karačić
- Surgery Clinic, University Hospital Sveti Duh, 10000 Zagreb, Croatia
| | - Marcela Konjevod
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000 Zagreb, Croatia
| | | | | | - Martina Luksic
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Hospital Sveti Duh, 10000 Zagreb, Croatia
| | - Neven Žarković
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000 Zagreb, Croatia
- Correspondence: (N.Ž.); (M.J.)
| | - Morana Jaganjac
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000 Zagreb, Croatia
- Correspondence: (N.Ž.); (M.J.)
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16
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Network pharmacology combined with GEO database identifying the mechanisms and molecular targets of Polygoni Cuspidati Rhizoma on Peri-implants. Sci Rep 2022; 12:8227. [PMID: 35581339 PMCID: PMC9114011 DOI: 10.1038/s41598-022-12366-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/10/2022] [Indexed: 11/08/2022] Open
Abstract
Peri-implants is a chronic disease leads to the bone resorption and loss of implants. Polygoni Cuspidati Rhizoma (PCRER), a traditional Chinese herbal has been used to treat diseases of bone metabolism. However, its mechanism of anti-bone absorption still remains unknown. We aimed to identify its molecular target and the mechanism involved in PCRER potential treatment theory to Peri-implants by network pharmacology. The active ingredients of PCRER and potential disease-related targets were retrieved from TCMSP, Swiss Target Prediction, SEA databases and then combined with the Peri-implants disease differential genes obtained in the GEO microarray database. The crossed genes were used to protein–protein interaction (PPI) construction and Gene Ontology (GO) and KEGG enrichment analysis. Using STRING database and Cytoscape plug-in to build protein interaction network and screen the hub genes and verified through molecular docking by AutoDock vina software. A total of 13 active compounds and 90 cross targets of PCRER were selected for analysis. The GO and KEGG enrichment analysis indicated that the anti-Peri-implants targets of PCRER mainly play a role in the response in IL-17 signaling, Calcium signaling pathway, Toll-like receptor signaling pathway, TNF signaling pathway among others. And CytoHubba screened ten hub genes (MMP9, IL6, MPO, IL1B, SELL, IFNG, CXCL8, CXCL2, PTPRC, PECAM1). Finally, the molecular docking results indicated the good binding ability with active compounds and hub genes. PCRER’s core components are expected to be effective drugs to treat Peri-implants by anti-inflammation, promotes bone metabolism. Our study provides new thoughts into the development of natural medicine for the prevention and treatment of Peri-implants.
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17
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Qiao L, Han J, Wang G, Yuan T, Gu Y. Promising novel biomarkers and candidate drugs or herbs in Osteoarthritis: Evidence from bioinformatics analysis of high‐throughput data. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220331090947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The most common joint illness is osteoarthritis (OA). The goal of this work was to find changes in gene signatures between normal knee joints and OA tissue samples and look for prospective gene targets for OA.
Methods:
The gene expression profiles of GSE12021, GSE51588, and GSE55457 were downloaded from Gene Expression Omnibus (GEO). Total 64 samples (40 OA and 24 standard control samples) were used. The limma program was used to find differentially expressed genes (DEGs) in OA versus NC. Functional annotation and protein-protein interaction (PPI) network construction of OA-specific DEGs were performed. Finally, the candidate drugs and herbs as potential drugs to treat OA were predicted in the DGIdb and TCMIO databases.
Results:
19 upregulated and 27 downregulated DEGs between OA and NC samples. DEGs such as PTN, COMP, NELL1 and MN1 have shown a significant correlation with OA and are expected to become new biomarkers. Cellular senescence,Positive regulation of ossification and Vascular endothelial growth factor (VEGF) were significantly enriched for OA‐specific DEGs.In cell composition analysis, DEGs were also found to be highly enriched in the cytosol.We have identified a total of 68 types of drugs or molecular compounds that are promising to reverse OA-related DEGs.Honeycomb and cinnamon oil have the possibility of treating OA.
Conclusion:
Our findings suggest new biomarkers that can be used to diagnose OA. Furthermore, we tried to find drugs and traditional Chinese medicine that may improve the progress of OA. This research may improve the identification and treatment of these uncontrollable chronic diseases.
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Affiliation(s)
- Linghui Qiao
- The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, China
| | - Jie Han
- Wuxi No.2 People\'s Hospital,Affiliated Wuxi Clinical College of Nantong University, China
| | - Guancheng Wang
- The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, China
| | - Tao Yuan
- The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, China
| | - Yanglin Gu
- The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, China
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Song Y, Zhang J, Wang H, Guo D, Yuan C, Liu B, Zhong H, Li D, Li Y. A novel immune-related genes signature after bariatric surgery is histologically associated with non-alcoholic fatty liver disease. Adipocyte 2021; 10:424-434. [PMID: 34506234 PMCID: PMC8437528 DOI: 10.1080/21623945.2021.1970341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Increasing evidence shows that immune-related genes (IRGs) play an important role in bariatric surgery (BS). We identified differentially expressed immune-related genes (DEIRGs) of adipose tissue after BS by analysing the two expression profiles of GEO (GSE59034 and GSE29409). Subsequently, enrichment analysis, GSEA and PPI networks were examined to identify the hub IRGs and related pathways. The performance of the signature was evaluated by area under the curve (AUC) of the receiver operating characteristic (ROC). CIBERSORT algorithm was used to evaluate the relative abundance of infiltrated immune cells.42 DEIRGs were found between the GSE59034 and GSE29409 datasets. The AUC of the signature was 0.904 and 0.865 in the GSE58979 and GSE48452, respectively. Interestingly, the signature also showed good performance in diagnosing non-alcoholic fatty liver disease (NAFLD) (AUC was 0.834 and 0.800, respectively). The number of neutrophils, macrophages M2, macrophages M0 and dendritic cells activated decreased significantly. After BS, the infiltration of T cells regulatory, monocytes, mast cells resting and plasma cells in adipose tissue increased. The novel proposed IRGs signature reveals the underlying immune mechanism of BS and is a promising biomarker for distinguishing the severity of NAFLD. This will provide new insights into strategies for treating obesity and NAFLD.
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Affiliation(s)
- Yancheng Song
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jan Zhang
- Department of Colonretal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Hexiang Wang
- Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dong Guo
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chentong Yuan
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Bo Liu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hao Zhong
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dongmei Li
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yu Li
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
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de Sousa ART, Freitas Junior WR, Perez EA, Ilias EJ, Silva AS, Alves VLS, Afonso JPR, Oliveira MC, Fonseca AL, da Silva MM, Lino MEM, Oliveira Junior MC, Vieira RP, Pedro WJS, Bachi ALL, Insalaco G, Malheiros CA, Oliveira LVF. Surgery for Obesity and Weight-Related Diseases Changes the Inflammatory Profile in Women with Severe Obesity: a Randomized Controlled Clinical Trial. Obes Surg 2021; 31:5224-5236. [PMID: 34554379 DOI: 10.1007/s11695-021-05702-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION/PURPOSE Obesity increases significantly every year worldwide. Since 1980, the prevalence of individuals with obesity has practically doubled. Obesity plays an important role in the pathophysiology of diseases that arise from a complex interaction of nutritional, genetic, and metabolic factors, characterizing a chronic inflammatory state. This study aimed to verify the systemic inflammatory response through the analysis of IGF-1, IL-23, and resistin levels and the lipid profile in severely obese women undergoing surgery for obesity and weight-related diseases. MATERIALS AND METHODS This randomized controlled clinical trial includes female patients clinically diagnosed with severe obesity with an indication for bariatric surgery. RESULTS In the initial evaluation, no significant difference was observed between the control (CG) and bariatric surgery (BSG) groups. The weight, BMI, systolic and diastolic blood pressures, total cholesterol, LDL, HDL, total non-HDL cholesterol, and glucose in BSG patients showed a significant change after surgery. Pre- and post-surgery levels of resistin, IGF-1, and IL-23 showed a significant difference in the BSG group, but only IL-23 was changed after 6 months in the CG. CONCLUSION The results of this study confirmed that weight loss induced by surgery for obesity and weight-related diseases improved the lipid profile and reduced the chronic inflammatory status in women with severe obesity.
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Affiliation(s)
| | | | - Eduardo Araujo Perez
- Post Graduation Program in Health Sciences, Santa Casa of Sao Paulo Medical School, Sao Paulo, SP, 01221-010, Brazil
| | - Elias Jirjoss Ilias
- Post Graduation Program in Health Sciences, Santa Casa of Sao Paulo Medical School, Sao Paulo, SP, 01221-010, Brazil
| | - Anderson Soares Silva
- Post Graduation Program in Health Sciences, Santa Casa of Sao Paulo Medical School, Sao Paulo, SP, 01221-010, Brazil
| | - Vera Lucia Santos Alves
- Post Graduation Program in Health Sciences, Santa Casa of Sao Paulo Medical School, Sao Paulo, SP, 01221-010, Brazil
| | - João Pedro Ribeiro Afonso
- Human Movement and Rehabilitation Post-Graduation Program, Evangelical University of Goiás (UniEVANGELICA), Anápolis, GO, 75083-515, Brazil
| | - Miriã Cândida Oliveira
- Human Movement and Rehabilitation Post-Graduation Program, Evangelical University of Goiás (UniEVANGELICA), Anápolis, GO, 75083-515, Brazil
| | - Adriano Luís Fonseca
- Human Movement and Rehabilitation Post-Graduation Program, Evangelical University of Goiás (UniEVANGELICA), Anápolis, GO, 75083-515, Brazil
| | - Marcos Mota da Silva
- Human Movement and Rehabilitation Post-Graduation Program, Evangelical University of Goiás (UniEVANGELICA), Anápolis, GO, 75083-515, Brazil
| | - Maria Eduarda Moreira Lino
- Human Movement and Rehabilitation Post-Graduation Program, Evangelical University of Goiás (UniEVANGELICA), Anápolis, GO, 75083-515, Brazil
| | - Manoel Carneiro Oliveira Junior
- Brazilian Institute of Teaching and Research in Pulmonary and Exercise Immunology (IBEPIPE), São José dos Campos, SP, 12245-520, Brazil
| | - Rodolfo Paula Vieira
- Brazilian Institute of Teaching and Research in Pulmonary and Exercise Immunology (IBEPIPE), São José dos Campos, SP, 12245-520, Brazil
- Postgraduate Program in Bioengineering, Universidade Brasil, São Paulo, SP, 08230-030, Brazil
| | - Wilson José Sena Pedro
- Clínica de Gastroenterologia e Medicina Avançada (GASTROMED), Anápolis, GO, 75080-620, Brazil
| | - André Luis Lacerda Bachi
- Brazilian Institute of Teaching and Research in Pulmonary and Exercise Immunology (IBEPIPE), São José dos Campos, SP, 12245-520, Brazil
- Department of Otorhinolaryngology, ENT Lab, Federal University of São Paulo (UNIFESP), São Paulo, SP, 04021-001, Brazil
- Post-Graduation Program in Health Science, Santo Amaro University (UNISA), São Paulo, SP, 04743-030, Brazil
| | - Giuseppe Insalaco
- Institute for Biomedical Research and Innovation, National Research Council of Italy (CNR), 90146, Palermo, Italy
| | - Carlos Alberto Malheiros
- Post Graduation Program in Health Sciences, Santa Casa of Sao Paulo Medical School, Sao Paulo, SP, 01221-010, Brazil
| | - Luis Vicente Franco Oliveira
- Post Graduation Program in Health Sciences, Santa Casa of Sao Paulo Medical School, Sao Paulo, SP, 01221-010, Brazil.
- Human Movement and Rehabilitation Post-Graduation Program, Evangelical University of Goiás (UniEVANGELICA), Anápolis, GO, 75083-515, Brazil.
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Luo C, Zhou X, Wang L, Zeng Q, Fan J, He S, Zhang H, Wei A. Screening and identification of NOTCH1, CDKN2A, and NOS3 as differentially expressed autophagy-related genes in erectile dysfunction. PeerJ 2021; 9:e11986. [PMID: 34447638 PMCID: PMC8366525 DOI: 10.7717/peerj.11986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
Background Loss of function of key autophagy genes are associated with a variety of diseases. However specific role of autophagy-related genes in erectile dysfunction ED remains unclear. This study explores the autophagy-related differentially expressed genes (ARGs) profiles and related molecular mechanisms in Corpus Cavernosum endothelial dysfunction, which is a leading cause of ED. Methods The Gene Expression Omnibus (GEO) database was used to identify the key genes and pathways. Differentially expressed genes (DEGs) were mined using the limma package in R language. Next, ARGs were obtained by matching DEGs and autophagy-related genes from GeneCard using Venn diagrams. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of ARGs were described using clusterProfiler and org.Hs.eg.db in R. Moreover, hub ARGs were screened out through protein-protein interaction (PPI), gene-microRNAs, and gene-transcription factors (TFs) networks then visualized using Cytoscape. Of note, the rat model of diabetic ED was established to validate some hub ARGs with qRT-PCR and Western blots. Results Twenty ARGs were identified from four ED samples and eight non-ED samples. GO analysis revealed that molecular functions (MF) of upregulated ARGs were mainly enriched in nuclear receptor activity. Also, MF of downregulated ARGs were mainly enriched in oxidoreductase activity, acting on NAD(P)H and heme proteins as acceptors. Moreover, six hub ARGs were identified by setting high degrees in the network. Additionally, hsa-mir-24-3p and hsa-mir-335-5p might play a central role in several ARGs regulation, and the transcription factors-hub genes network was centered with 13 ARGs. The experimental results further showed that the expression of Notch1, NOS3, and CDKN2A in the diabetic ED group was downregulated compared to the control. Conclusions Our study deepens the autophagy-related mechanistic understanding of endothelial dysfunction of ED. NOTCH1, CDKN2A, and NOS3 are involved in the regulation of endothelial dysfunction and may be potential therapeutic targets for ED by modulating autophagy.
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Affiliation(s)
- Chao Luo
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiongcai Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Department of Urology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Wang
- School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong, China
| | - Qinyu Zeng
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Junhong Fan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shuhua He
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Haibo Zhang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Anyang Wei
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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